From ff011fbe01311eaaa08e0dc9efccdc85a8a6c987 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 20 Mar 2025 16:24:58 -0400 Subject: [PATCH] Handle directories with percents in export_remote.xml. --- lib/galaxy/tools/parameters/basic.py | 8 ++++++ test/integration/test_remote_files.py | 40 +++++++++++++++++++++++++++ tools/data_export/export_remote.py | 16 +++++++++-- tools/data_export/export_remote.xml | 3 +- 4 files changed, 63 insertions(+), 4 deletions(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 18329f486ec..696b992b2da 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2669,6 +2669,14 @@ class DirectoryUriToolParameter(SimpleTextToolParameter): if not user_has_access: raise ParameterValueError(f"The user cannot access {value}.", self.name) + def to_param_dict_string(self, value, other_values=None) -> str: + """Called via __str__ when used in the Cheetah template""" + if value is None: + value = "" + elif not isinstance(value, str): + value = str(value) + return value + class RulesListToolParameter(BaseJsonToolParameter): """ diff --git a/test/integration/test_remote_files.py b/test/integration/test_remote_files.py index c56759bb6f7..6ac53a15550 100644 --- a/test/integration/test_remote_files.py +++ b/test/integration/test_remote_files.py @@ -205,6 +205,46 @@ class TestRemoteFilesIntegration(ConfiguresRemoteFilesIntegrationTestCase): with open(os.path.join(ftp_dir, "my_cool", "utf8_name_😻.txt")) as f: assert "example content\n" == f.read() + def test_export_remote_tool_with_space(self): + dataset_populator = self.dataset_populator + ftp_dir = self.user_ftp_dir + _write_file_fixtures(self.root, ftp_dir) + dir_with_space = os.path.join(ftp_dir, "space dir") + os.makedirs(dir_with_space) + with dataset_populator.test_history() as history_id: + dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo") + infile = {"src": "hda", "id": dataset["id"]} + inputs = { + "d_uri": "gxftp://space dir/", + "export_type|export_type_selector": "datasets_named", + "export_type|datasets_0|infile": infile, + "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt", + } + response = dataset_populator.run_tool("export_remote", inputs, history_id) + dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True) + with open(os.path.join(ftp_dir, "space dir", "my_cool", "utf8_name_😻.txt")) as f: + assert "example content\n" == f.read() + + def test_export_remote_tool_with_space_encoded(self): + dataset_populator = self.dataset_populator + ftp_dir = self.user_ftp_dir + _write_file_fixtures(self.root, ftp_dir) + dir_with_space = os.path.join(ftp_dir, "space%20dir") + os.makedirs(dir_with_space) + with dataset_populator.test_history() as history_id: + dataset = dataset_populator.new_dataset(history_id, content="example content", wait=True, name="foo") + infile = {"src": "hda", "id": dataset["id"]} + inputs = { + "d_uri": "gxftp://space%20dir/", + "export_type|export_type_selector": "datasets_named", + "export_type|datasets_0|infile": infile, + "export_type|datasets_0|name": ".my_cool/utf8_name_😻.txt", + } + response = dataset_populator.run_tool("export_remote", inputs, history_id) + dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True) + with open(os.path.join(ftp_dir, "space%20dir", "my_cool", "utf8_name_😻.txt")) as f: + assert "example content\n" == f.read() + def test_export_remote_tool_default_duplicate_name_fails(self): dataset_populator = self.dataset_populator ftp_dir = self.user_ftp_dir diff --git a/tools/data_export/export_remote.py b/tools/data_export/export_remote.py index 6574756a85f..f0b027e5a92 100644 --- a/tools/data_export/export_remote.py +++ b/tools/data_export/export_remote.py @@ -35,15 +35,23 @@ def write_if_not_exists(file_sources, target_uri, real_data_path): file_source.write_from(file_source_path.path, real_data_path) +def get_directory_uri(args): + directory_uri = args.directory_uri + if not directory_uri: + inputs = json.load(open(args.inputs, "r")) + directory_uri = inputs["d_uri"] + if not directory_uri.endswith("/"): + directory_uri = f"{directory_uri}/" + return directory_uri + + def main(argv=None): if argv is None: argv = sys.argv[1:] args = _parser().parse_args(argv) exit_code = 0 file_sources = get_file_sources(args.file_sources) - directory_uri = args.directory_uri - if not directory_uri.endswith("/"): - directory_uri = f"{directory_uri}/" + directory_uri = get_directory_uri(args) export_metadata_files = args.export_metadata_files with open(args.files_to_export) as f: files_to_export = json.load(f) @@ -68,6 +76,8 @@ def main(argv=None): def _parser(): parser = argparse.ArgumentParser() + parser.add_argument("--inputs", type=str, help="galaxy inputs") + # post 2026.XX drop the directory-uri argument and just assume inputs always contains d_uri. parser.add_argument("--directory-uri", type=str, help="directory target URI") parser.add_argument("--file-sources", type=str, help="file sources json") parser.add_argument("--files-to-export", type=str, help="files to export") diff --git a/tools/data_export/export_remote.xml b/tools/data_export/export_remote.xml index fe544c48e20..63f2318a6c5 100644 --- a/tools/data_export/export_remote.xml +++ b/tools/data_export/export_remote.xml @@ -8,7 +8,7 @@ + #import json #from galaxy.util import filesystem_safe_string #if $export_type.export_type_selector == "datasets_auto":